Well, you mention lots of issues, I'll try to reply, but I don't promise that it will be brief: throwing spurious claims requires fewer words than refuting them.
If you allow me an aside, I find again in your last post the same kind of language and cliches that I would expect from a liberal American professor.
"Medieval tyrant" - somehow the age of Saint Francis of Assisi, Saint Louis of France, Saint Elizabeth of Hungary [I'm still waiting for the president of a republic or the first lady who washes the feet of beggars or kisses the sores of lepers, Chartres Cathedral, Giotto, Dante, Le Morte d'Arthur... is a synonym of darkness, whereas the 20th century, the century of Holodomor, Auschwitz, the GULAG, Hiroshima, Nagasaki, the killing fields of Cambodia... is a bright century of progress.
"Nicholas was of the wrong side of history, as was Franz Josef and the Kaiser". I like your historical determinism: everything that happened was bound to happen, History is a stream that flows in a certain direction and you cannot oppose it. Kind of marxism or Fukuyama-style liberalism.
Regarding antisemitism and pogroms. If I said that Woodrow Wilson or FDR tolerated or promoted the lynching of blacks in the Southern States of the USA or the Ku Kux Klan, you would correctly reply that's slander because there is no base to make that claim. And Wilson and FDR were presidents when those crimes took places. And the governors of the States where those crimes took place (and where discriminatory- racist laws against blacks were enforced) belonged to the same political party of Wilson and FDR. But somehow when we discuss the tsarist regime we can allow us to use different standards, can't we?
In a letter to Kostantin Romanov (14.09.1912), Nicholas II writes that he shares the opinion of the Holy Synod that KR's play The King of Judea cannot be publicly staged because the theme (Christ's Passion) might provoke pogroms. That is not the behaviour of a hatemonger.
The Jews suffered discriminatory laws, which forbade them to live beyond the Pale of Settlement, certain professions and set quotes to access to university. Certainly unfair, but it was religious, not racially-motivated discrimination. A Jew who became Orthodox was accepted immediately as a Russian, exactly with the same rights (a possibility that a black man in Alabama or in British-administered South Africa didn't have). The tsarist regime was no forerunner of Hitler's Holocaust.
As I have said the situation was unfair and probably laws against Jews would have been done away with or at least ameliorated if Nicholas II had not had to contend with a revolutionary movement, a World War and irresponsible Duma politicians.
A letter of Alexandra to Nicholas dated 7.04.1916 (emphasis is mine):
"I send you the petition of one of Aunt Olga's wounded men. He is a Jew. Has lived since 10 years in America. He was wounded and lost his left arm on the Carpathians. The wound has healed well, but he suffers fearfully morally as in August he must leave, and loses the right of living in either the capital or other big town. He is living in town only on the strength of a special permit, which a previous minister of the Interior gave him for one year. And he find work in a big town.
His English is wondefully good. I read a letter of his to little Vera's English governess and Aunt Olga says he is a man with good education, so to speak. 10 years ago he left for the United States to find the opportunity to become a useful member of human society to the fullest extend of his capacities, as here it is difficult for a Jew who is always hampered by legislative restrictions. Tho' in America, he never forgot Russia and suffered much from homesickness and the moment the war broke out he flew here to enlist as soldier to defend his country.
Now that he lost his arm seving in our amy, got the St George Medal, he longs to remain here and have the right to live wherever he pleases in Russia, a right the Jews don't possess. As soon as discharged from the army, as a criplle, he find things have remained the same as before, and his headlong rush home to fight, and loss of his arm has brought him no gain. One sees the bitterness, and I fully grasp it - surely such a man ought to be treated the same as any other soldier who received such a wound. He was not obligued to fly over here at once. Tho' he is a Jew, one would like him to be justly treated and not different t the others with similar losses of limb.
With his knowledge of English and learning he could easier gain his bread in a big town of course; and one ought not let him become more bitter and feel the cruelty of his old country. To me it seems hard upon all - it's so cruel to my mind. The bad ones can be severely punished. Can you tell me what decision you write on the petition; as aunt Olga wanted to know."
Nicky to Alix - 7 April
"I wrote on the petition of the wounded jew from America - to allow living in any place of Russia and sent it to Sturmer."
The role of the Tsar in the ROC:
Unless you belong to the ROC (I think you don't), that's not a matter you have a say on. I am a Catholic and I can tell you how irritating is to read how people who aren't Catholic, or Christian or believe in God decide what the Pope must do or what beliefs we Catholics have to dispose of in order to become acceptable to their eyes.
The democratic institutions being shut down
Can you point one? Do you mean the Duma? Who did represent there the peasants, 80% of Russian population? The terrorist Socialist-Revolutionaries? The marxist revolutionaries who thought that they were "petty bourgeoisie"? The liberal Constitutional Democrats (who kept a friendly attitude towards revolutionary terrorism)? The Octobrists, the party of industrialists and members of the liberal professions leaded by Gukchov, the man who had no qualms about associating himself with a blackmailer to get Alexandra's "Rasputin letters"?
Did they behave in a responsible way during the war or indeed before the war? Did they behave in a honourable way when they asked (and got) the head of Myasoyedov (a kind of Russian Dreyfuss Affair), an innocent man who was accused of being a spy for the Germans and executed because he belonged to the corps of gendarmes that liberals hated?